i think you should have called the short stack's all in. That way if the chipleader called, you would have had a chance to fold on the flop when there was an Ace and CL showed aggression.

I had a similar situation, in the same tourney as you. my stack was 5bb's and blinds were killing me, UTG raised, i had JJ. i hoped for an AK or AQ and went all in. He had QQ.